WBPaper00052881:B.subtilis-biofilm_upregulated

CuffDiff q-value < 0.05. Transcripts that showed significantly increased expression after the formation of B. subtilis biofilm

WBPaper00052881:B.subtilis-biofilm_downregulated

CuffDiff q-value < 0.05. Transcripts that showed significantly decreased expression after the formation of B. subtilis biofilm

WBPaper00064565:dyf-1(mn335)_regulated_protein

FDR < 0.1 Significantly affected proteins in dyf-1(mn335) compared with wild-type (q-value cut off 0.1)

WBPaper00060014:set-2(tm1630)_upregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(zr2012)_downregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly decreased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(zr2012)_upregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly increased expression in set-2(zr2012) animals at embryo stage, comparing to in N2 animals.

WBPaper00060014:set-2(tm1630)_downregulated

DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. Transcripts that showed significantly decreased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals.

WBPaper00042477:RSR-2_complex

Percolator (semi-supervised learning machine) was used at constant 0.01% FDR. Percolator assigns a q-value to each spectrum, which is defined as the minimal FDR at which the identification is deemed correct. These q values are estimated using the distribution of scores from decoy database search, and the q-value threshold was set to <0.01 to validate any peptide. Proteins contained in RSR-2 complex, according to immunoprecipitation using anti-RSR-2, and MudPIT, liquid chromatography and mass spectrometry.

WBPaper00051388:Glucose-diet_upregulated

CuffDiff, q-value < 0.05 Transcripts that showed significantly increased expression in NGM+Glucose diet for 20h at 20C, comparing to in NGM.

WBPaper00058925:acox-1.1(ok2257)_downregulated

DESeq2, q-value < 0.01 Transcripts that showed significantly decreased expression in acox-1.1(ok2257) comparing to in N2 at L4 larva stage.